Antimicrobial Potential of Natural Compounds of Zingiberaceae Plants and their Synthetic Analogues: A Scoping Review of In vitro and In silico Approaches

Aims: There has been increased scientific interest in bioactive compounds and their synthetic derivatives to promote the development of antimicrobial agents that could be used sustainably and overcome antibiotic resistance. Methods: We conducted this scoping review to collect evidence related to the antimicrobial potential of diverse natural compounds from Zingiberaceae plants and their synthetic derivatives. We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Extension for Scoping Reviews guidelines. The literature search was conducted using PubMed, Web of Science and Scopus electronic databases for relevant studies published from 2012 to 2023. A total of 28 scientific studies fulfilled the inclusion criteria. The authors of these studies implemented in vitro and in silico methods to examine the antimicrobial potency and underlying mechanisms of the investigated compounds. Results: The evidence elucidates the antimicrobial activity of natural secondary metabolites from Zingiberaceae species and their synthetic derivatives against a broad panel of gram-positive and gram-negative bacteria, fungi and viruses. Conclusion: To date, researchers have proposed the application of bioactive compounds derived from Zingiberaceae plants and their synthetic analogues as antimicrobial agents. Nevertheless, more investigations are required to ascertain their efficacy and to broaden their commercial applicability.


INTRODUCTION
Herbs have been utilised for medical and culinary purposes for thousands of years.Recent advancements necessitate increased research efforts to identify pharmacologically active herbal plants and their bioactive compounds for phytotherapy [1].Due to their historical use as medicines, plants of Zingiberaceae (the ginger family) are gaining popularity among the public.Zingiberaceae is the most prominent family within the order Zingiberales; its members include diverse bioactive constituents with great ethnopharmacological value [2].This family covers more than 50 genera, with 1300 species, and is widespread in tropical and subtropical climates, with the most remarkable diversity in South and Southeast Asia [3,4].Several genera of this family, including Alpinia, Zingiber, Curcuma, Hedychium, Amomum, Elettaria and Kaempferia, are renowned for their medicinal pro-perties, as exemplified by Javanese ginger (Curcuma xanthorrhiza D.Dietr.), turmeric (Curcuma longa L.), galangal (Alpinia galanga L.) and ginger (Zingiber officinale Roscoe) [2].
The aromatic flowering plants in this family exhibit horizontal or creeping tuberous rhizomes and are globally applied as perennial herbs for various purposes.Indeed, due to their aromatic odours and pungent characteristics, these plants have served extensively as spices and/or flavouring agents.The rhizomes are characterised by their capacity to segment and display sympodial branching.The colour of the rhizomes can distinguish distinct species, ranging from pale yellow to dark yellow, greenish-blue, pink or a combination of these colours [5].The rhizomes usually harbour leaves arranged in a transverse or parallel fashion, with morphologically varied structures, shapes and sizes.The Zingiberaceae plants mainly express small or large labellum, lateral staminodes, narrow and long filaments, and unilocular or trilocular ovaries [5].In the following paragraphs, we introduce several genera and species of Zingiberaceae, including their pur-ported therapeutic purposes, putative biological activity and bioactive constituents.
Curcuma species have been used for centuries to address discrete health complications.The major bioactive components of Curcuma rhizomes are non-volatile curcuminoids, as well as volatile sesquiterpenoids and monoterpenoids (Fig. 2).Curcuminoids include curcumin, demethoxycurcumin and bisdemethoxycurcumin.Both demethoxycurcumin and bisdemethoxycurcumin are curcumin analogues, and these three compounds are the polyphenols responsible for the yellow pigmentation of turmeric rhizomes [18].On the other hand, sesquiterpenoids and monoterpenoids are the main classes of compounds found in essential oils.Curcuma essential oils have been promoted as ideal candidates for manufacturing pharmaceutical and cosmetic products due to their antioxidant and antimicrobial properties [19].C. longa, commonly referred to as turmeric, has a wide range of pharmacological activities -including anticancer and anti-inflammatory -due to its high curcumin content [20,21].Alpinia, has been investigated for its biological activities, including combating pathogenic microbes and treating severe infections and diseases.Phytochemical analysis has indicated the presence of diarylheptanoids, terpenes including sesquiterpenoids and monoterpenes, and flavonoids in this genus (Fig. 3).These compounds possess anti-inflammatory, hepatoprotective, antioxidant and anticancer effects [22].There are five characteristic subtypes of diarylheptanoids, which are structurally distinct phenolic compounds, in this genus: linear, dimeric, cyclic, chalcone/flavanone and novel [23].Linear and chalcone/flavanone diarylheptanoids are commonly found in Alpinia species.Most of the research on this genus has focused on Alpinia galanga (L.) Willd.due to the higher number of bioactive compounds it contains compared with the other species of the genus, including alpha-fenchyl acetate, beta-bisabolene, beta-pinene, alpha-bergamotene, 1,8-cineole, 1′-acetoxychavicol acetate and beta-farnesene [24].The essential oil derived from dried and fresh A. galanga has shown to exert antimicrobial ef-fects on various bacteria, yeast, fungi and parasitic organisms [25].
Phenylpropanoids, often characterised as the prominent organic compounds in Etlingera volatile oils, are derived from phenylalanine and tyrosine precursors through the shikimic acid pathway.The presence of phenylpropanoids allows the plants to cope with biotic and abiotic stresses.Eugenol, (E)-methyl isoeugenol, methyl eugenol, elemicin and methyl chavicol are the most researched phenylpropanoids in Etlingera species [26].Etlingera elatior (Jack) R.M.Sm. is widely cultivated in Southeast Asia and substantially applied for decorative and culinary purposes in Malaysian and Thai communities [27].Etlingera coccinea  (Blume) S.Sakai & Nagam., which is endemic to Borneo, has been used to treat gastrointestinal complications in folk medicine [27].The essential oils derived from Etlingera fimbriobracteata (K.Schum.)R.M.Sm [28], E. elatior [29], Etlingera sayapensis A.D. Poulsen & Ibrahim [30] and Etlingera pavieana (Pierre ex Gagnep.)R.M.Sm [31], as well as the crude extracts from E. coccinea [32], Etlingera sessilanthera R.M.Sm [32].and E. elatior [33], have been assessed regarding their antibacterial properties against a variety of gram-positive and gram-negative bacteria; they have demonstrated moderate to strong antibacterial activity.
Plants of the Amomum genus have traditionally been applied to treat stomach problems, oral infections, respiratory diseases, malaria, cancer and inflammatory conditions [34,35].The Amomum genus has been explored for its principal compounds, such as flavonoids, terpenoids and diarylheptanoids, and up to 160 compounds have been isolated and their biological activities have been discussed (Fig. 5) [34].These efficacious phytochemicals contribute to their antimicrobial, antioxidant and antiallergic properties [34].Furthermore, the phytochemical profiles of Amomum volatile oils have revealed the limonene, 1,8-cineole, camphor, alpha-pinene, caryophyllene, santolina triene, bornyl acetate, beta-elemene, delta-3-carene, allo-aromadendrene, farnesyl acetate, methyl chavicol, D-camphor, beta-pinene and camphene as the major compounds [35].Amomum subulatum Roxb., usually referred to as black cardamom or the 'Queen of Spices', is one of the essential commercial crops of the Himalayan region and is exploited for its medicinal values in managing various respiratory illnesses [36].In traditional Asian medicine, the Kaempferia genus has been proved to cure distinct ailments, such as wound infection, cough, infectious diseases, and gastrointestinal disorders [37].The plants of this genus contain the usual secondary metabolites of the other Zingiberaceae genera, such as phenolic compounds, flavonoids, diterpenoids and volatile oils (Fig. 6).The isopimarane-type diterpenoids are the most abundant in this genus with inspected anti-inflammatory activity, whereas steroids are a minor class of natural compounds in Kaempferia species [38].The essential oils derived from this species comprise phenylpropanoids and cinnamates as the main secondary metabolites, followed by monoterpenes.Kaempferia galanga L., the representative species in this genus, possesses pharmacological and curative functions attributed to trans-ethyl cinnamate and pmethoxycinnamate in the extracted essential oils [39].Hence, owing to the presence of various constituent classes in Kaempferia volatile oils, they are especially involved in antimicrobial and antioxidant activities [40].
The antimicrobial activity of Zingiberaceae plant extracts and essential oils has been critically reviewed.However, there has not been a comprehensive scoping review discussing the antimicrobial properties of the individual plant-derived or synthetic bioactive compounds from Zingiberaceae plants.Increasing evidence-based scientific knowledge regarding compounds with antimicrobial properties can ensure the development and use of medicinal plant-based products.Therefore, in this review, we discuss the characteristics of relevant studies that involve the Zingiberaceae species; the types of studies; the compounds analysed; the methods used for the detection, isolation, characterisation or synthesis of compounds; and the assessment of antibacterial, antifungal and antiviral activities.

Eligibility Criteria
This review only includes published studies.We selected studies in English that discussed the antibacterial, antifungal and/or antiviral activities of natural biologically active compounds from Zingiberaceae plants and their synthetic derivatives against human pathogenic microbes.

Information Sources
We searched the Web of Science, Scopus and PubMed databases for suitable articles published from 2012 to 2023.The primary reason for limiting the search period was to obtain up-to-date evidence on the antimicrobial properties of natural bioactive compounds and related synthetic analogues.

Search Strategy
In the first stage, we used suitable keywords -'Bioactive compound', 'Zingiberaceae' and 'Antimicrobial' with suitable Boolean operators AND/OR and truncation symbol $to search the selected databases (Table 1).

Study Selection Process
We excluded several studies from the search results, including review articles, case reports, conference proceedings, protocol papers and book reviews.Duplicate records were eliminated with the help of EndNote version 20.Moreover, we screened the titles and abstracts of the publications and assessed them by using the inclusion criteria to select the content that could answer the objectives.Referring to the selected titles and abstracts, the full-text articles were critically appraised to determine which articles could be used for ongoing analysis and included in this scoping review.

Data Charting
In the third stage, we extracted the necessary information from the chosen articles.Two authors independently examined the derived data, and any discrepancies were resolved through a consensus discussion.A data-charting form was created in Excel.The two authors reviewed the findings and revised the data charting form.

Data Items
The data extracted from each article included the authors, year of publication, study type, Zingiberaceae species, compounds, methodology, bacterial/fungal/viral species, antibacterial/antifungal/antiviral activity, and study outcomes as sorted out in the supplementary material (Tables S1-S3).The study types were in vitro, in silico or a combination of both.We authenticated the taxonomic information of the Zingiberaceae species by using the World Flora Online (WFO) database.The methodology involved compound iso-lation, synthesis and characterisation, and antimicrobial assays.The two authors only included compounds with positive antimicrobial activity for in vitro studies or those that displayed notable binding energy and documented interaction with targets for in silico research.

Selection of Sources of Evidence
As shown in Fig. (8), our database searches yielded 317 titles.There were two duplicates, so we screened the title and abstract of 315 records for eligibility, whereby 277 studies were omitted, leaving 38 articles.Two studies could not be retrieved; thus, 36 articles progressed to the subsequent comprehensive full-text review.Finally, we extracted data from 28 articles that satisfied the inclusion criteria and answered the research question of this scoping review.The rationale for the exclusion of the eight articles was: three solely discussed crude extracts, essential oils or bioactive fractions but not individual compounds; one used undefined reporting units of antibacterial and antifungal activities; one did not mention the antimicrobial assay performed; one used phytopathogen as the study target; one reported the synergistic effect of the compound with other agents, without testing a single compound; and one reported negative results of the tested compounds.

General Characteristics of the Included Studies
Out of the included 28 articles, 18 studies involved only in vitro experiments, 7 discussed only in silico analyses and 3 conducted both in vitro and silico analyses.Eight studies were carried out in India, four in Malaysia, four in Indonesia, two in China, two in the United Kingdom, two in Japan, two in the Republic of Korea, and one each in Saudi Arabia, Iran, Brazil and Vietnam.
All plants evaluated in the included studies are part of the Zingiberaceae family.Fig. (9) shows the distribution of the Zingiberaceae plant species involved in the included studies.Z. officinale (12 studies) was the most studied species, followed by Z. zerumbet   The included studies employed various methods to evaluate the antimicrobial potential of natural or synthetically produced compounds from Zingiberaceae plants (Fig. 11).
The broth microdilution method was the most prominent assay and the gold-standard reference method (14 studies) for determining the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) as indicators of antibacterial and antifungal properties.Several studies utilised diffusion tests, including the agar well (2 studies) and agar disk diffusion (1 study) techniques, to determine the inhibition zone as part of the screening test.The authors conducted in silico molecular docking simulations to investigate the interaction between phytochemicals and binding sites in bacteria and fungi and to propose the possible underlying antibacterial and antifungal mechanisms of those compounds (4 studies).Other methods, such as broth macrodilution (1 study), spot inoculation (1 study), the pour plate method (1 study), the microplate Alamar blue assay (1 study) and the low oxygen recovery assay (1 study) were used to determine antibacterial and antifungal activities.
To appraise the antiviral properties of plant compounds, the studies most often used the molecular docking approach for in silico analyses (7 studies), with SARS-CoV-2 serving as the examined target.For the in vitro study of bioactive compounds against SARS-CoV-2, a 3CL protease inhibition assay (1 study) was performed.The cytopathic effect (CPE) assay (1 study) was also used to elucidate viral inhibition by compounds in vitro.

Assessment of the Main Study Outcomes
To investigate the antibacterial effects exerted by selective natural or synthetic compounds, 17 studies reported the activity against diverse species and strains.Seven of these studies explained the contribution of the chemical structures of the compounds to their antibacterial activity [45][46][47][48][49][50][51].Two studies reported that the antibacterial activity of purified compounds was superior to those of plant extracts and essential oils, even though the authors hypothesised that there is a synergistic interaction between the plethora of compounds identified through phytochemical screening [52,53].Two studies revealed that the compounds were less effective against gram-negative bacteria than against gram-positive bacteria [46,54], and one study disclosed the inability of the compound to inhibit the involved gram-negative bacteria with the tested concentration range [55].One study demonstrated the synergistic antibacterial effects of plant compounds and antibiotics [56].
Six studies evaluated the antifungal properties of active compounds.One study related antifungal activity to the structure of the compounds [45].One study reported that the killing effects of the compound on fungal strains were more effective than the commercial antifungal agent [57].One study demonstrated the enhanced antifungal effect of a plan-t-derived compound on another natural antifungal agent [58].In addition, one study reported that a single isolated compound had a superior antifungal effect than rhizome essential oils [53].The antiviral potential of plant compounds has been evaluated against several structural targets of SARS-CoV-2, including 3C-like protease (3CL pro ) or main protease (M pro ) [59][60][61], papain-like protease PL pro [61] and spike protein [62][63][64][65][66][67], showing the binding interaction between the compounds and target sites of SARS-CoV-2 via an in silico approach.
In another study, researchers isolated a diarylheptanoid named etlingerin (24) from E. pubescens and reported its bactericidal effect against S. aureus, B. cereus and B. subtilis (MIC = 0.0625-0.125 mg/mL; MBC = 0.0625-0.125 mg/mL) [55].The SYTO-9/propidium iodide uptake method indicated the detrimental effect of this compound on the bacterial membrane: it promoted the leakage of cellular content such as DNA and proteins based on the bacterial cellular leakage assay.
C. caesia Roxb.yielded the phenolic compound curcumin (25), the major curcuminoid present in turmeric, based on bioassay-guided isolation from crude methanolic root extract.The broth macrodilution sensitivity test showed that compared with the crude extract, curcumin exhibited lower MICs and MBCs against a panel of gram-positive Staphylococcus and Bacillus strains (MIC = 0.0625-0.25 mg/mL) and gram-negative K. pneumoniae, E. coli, P. aeruginosa and Proteus vulgaris (MIC = 0.25-1 mg/mL) [52].
Focussing on Z. officinale, two representative phenolic compounds -6-gingerol (30) and its dehydrated product 6shogaol (31) -showed moderate to potent antibacterial activity against gram-positive E. faecalis, B. subtilis and effluxing MRSA strains (MIC = 8-512 mg/L) and the gram-negative bacteria P. aeruginosa, E. coli, K. pneumoniae and Proteus sp.(MIC = 128-512 mg/L) [48].The lower activity against gram-negative bacterial species could be due to the permeability barrier to the antibacterial compounds or unfavourable structural modification of the compounds to reduce their activity.Nevertheless, the aliphatic side chain in 6-gingerol (30) and the presence of a double bond in 6-shogaol (31) account for their effective antibacterial activity.In the same study employing the broth mating method, the researchers noted that the anti-plasmid activity of 6-gingerol (30) and 6shogaol (31) actively hindered the transfer of resistant plasmids in E. coli (TP114, PUB 307 and PKM 101) that is facilitated by bacterial type IV secretion system, suggesting their potential as natural anti-plasmid agents that assist in overcoming antibiotic resistance.

Antifungal Properties
In vitro and in silico studies have been carried out to assess the antifungal properties of natural compounds from Zingiberaceae species and their synthetic derivatives to illuminate the structure-function relationship and to resolve the complex mechanisms of action.The authors synthesised dehydrozingerone (19) from Z. officinale and its derivatives (20)(21)(22)(23) via stepwise processes and examined their antifungal activity against Fusarim sp.Gt-1019, Penicillium sp., Aspergillus flavus, Aspergillus ochraceus, Aspergillus oryzae and Aspergillus niger by using the agar diffusion method; the inhibition zone was 15.0-31.5 mm at a dose of 1 mg [45].The authors stated that the carbonyl group confers antifungal efficacy to the compounds.The polarisation of the carbon-oxygen double bond in the aldehyde or keto group likely explains their ability to form covalent bonds with fungal DNA and proteins and to disrupt fungal metabolism.
Based on in silico molecular docking, serverogenin acetate (58) derived from A. nilgiricum also has antifungal potential [72].Among the 25 detected compounds in gas chromatography-mass spectrometry analysis, serverogenin acetate (58) showed the lowest binding energy with the fungal target 4i9p (-105.78kcal/mol) and displayed the best phytoligand-protein complex binding stability via hydrogen bonds with Thr170, Arg173, Ser504, Lys503, His502 and His469.Kim and Eom [57] interrogated the species-dependent antifungal effect of 6-shogaol (31) from Z. officinale.They applied this pungent ginger compound to several Candida clinical isolates, specifically Candida auris, Candida glabrata and Candida tropicalis.Apart from the intense inhibitory activity against the planktonic form of these fungi at 50% and 80% of the population (MIC 50 = 16 to >64 μg/mL; MIC 80 = 32 to >64 μg/mL), the compound also showed inhibitory and eradication effects of 80% of C. auris biofilm matrix at low concentrations (MBIC80 = 32-64 μg/mL; MBEC80 = 32 μg/mL).Confocal laser scanning microscopy of the pre-formed C. auris biofilms treated with 6-shogaol (31) revealed reduced levels of proteins, nucleic acids and carbohydrates in the biomass as well as a low cell density.The authors demonstrated the fungicidal properties of this compound in a time-kill assay, with a dose-dependent decrease in the viability of the fungal strains.Most importantly, the compound could decrease the expression of the CDR1 gene in C. auris, which is associated with efflux pump activity.Hence, this compound might be useful in clinical settings to address resistant fungal infection [57].Tian et al. [53] evaluated the antifungal activity of zerumbone ( 15) derived from Z. zerumbet against Candida albicans.The MIC and MBC were 31.25 and 250.00 μg/mL, respectively.Besides, 100 mg/mL zerumbone produced an inhibition zone of 11.31 ± 0.83 mm on the agar inoculated with C. albicans.This sesquiterpenoid is an active antifungal compound and mainly contributes to the antifungal activity of Z. zerumbet essential oil.
Yamano et al. [58] showed that dehydrozingerone (19) from Z. officinale improved the antifungal effects of glabridin, an isoflavane derived from the Glycyrrhiza glabra L. roots, against C. albicans and Saccharomyces cerevisiae in the checkerboard assay.The combined treatment markedly reduced the expression of the PDR1, PDR3 and PDR5 genes -which encode efflux pumps in S. cerevisiae -compared with glabridin alone.This compound also indirectly altered the translation of Pdr5p, an ABC transporter.Overall, these findings provide evidence for the use of combination therapy involving plant-derived compounds against drug-resistant fungi.

Antiviral Properties
In response to the coronavirus disease 2019 (COVID-19) pandemic, since 2020, researchers have employed in silico molecular docking in computer-aided drug design to evaluate many phytoligands identified from Zingiberaceae species as potential antiviral agents against SARS-CoV-2.Zubair et al. [60] proposed combining chromatographic/spectroscopic methods with docking analysis and molecular dynamics simulations to identify the potential antiviral bioac-tive compounds originating from Z. officinale.The authors found that three steroid compounds -24-methylcholesta-7-en-3β-on (69) (-68.80 kcal/mol), spinasterol (70) (-78.11kcal/mol) and spinasterone (71) (-87.4 kcal/mol)have a lower binding energy and a stronger binding affinity to the SARS-CoV-2 3CL protease.The 3CL protease represents a promising therapeutic target due to its role in regulating coronavirus replication.In the molecular docking analysis, the authors discussed several notable interactions between the compounds and 3CL protease amino acids, including a hydrogen bond between the hydroxyl group of spinasterol (70) and Thr190; a hydrogen bond between the carboxyl group of 24-methylcholesta-7-en-3β-on (69) and Cys44; and hydrophobic interaction between spinasterone ( 71) and Val42, Leu167, Cys44 and Pro168.The authors subsequently investigated the in vitro inhibitory effect of 24methylcholesta-7-en-3β-on (69) extracted from ginger pseudostem on SARS-CoV-2 3CL pro by performing an inhibition assay; there was 75% enzymatic inhibition at a concentration of 500 µM.The subsequent molecular dynamics simulation showed that 24-methylcholesta-7-en-3β-on ( 69) could bind to His41 and Cys145 in the catalytic site with a corresponding root mean square fluctuation (RMSF) of 0.755 and 0.880 Å, respectively.These findings underscore the inhibitory mechanism of 24-methylcholesta-7-en-3β-on (69) at the molecular level.
Wijaya et al. [66] determined that the phenolic compound 4-gingerol (72) from Z. officinale can target the SARS-CoV-2 main protease (also termed M pro or 3CL pro ).This compound showed the lowest binding energy (-7.3 kcal/mol) among the 16 investigated compounds and could interact with the main protease domains by hydrophobic bonding at Gln110, Phe294, Asn151 and Val104, as well as hydrogen bonding at Thr111, Asn151 and Asp153.As mentioned by the authors, the formation of hydrogen bonds is vital to facilitate ligand-protein interactions, protein folding and breakdown.Moreover, this compound did not violate Lipinski's rule of five, and the molecular dynamics simulation showed a stable ligand-protein complex conformation with an RMSF below 1-3 Å.
In a comprehensive study, Mehmood et al. [59] chose six distinct medicinal plants originating from different families to identify compounds with antiviral properties against SARS-CoV-2.Based on the docking analysis, the researchers highlighted a monoterpene (73) from Z. officinale because it interacted with the inhibitory drug targets RNA-dependent RNA polymerase (RdRP) that governs coronavirus replication, 3CL pro and angiotensin-converting enzyme 2 (ACE2) as the binding site of SARS-CoV-2 spike protein for subsequent replication.The authors selected this monoterpene (73) for docking analysis because it fulfilled Lipinski's rule of five, had previously reported antiviral activity, complied with absorption, distribution, metabolism, excretion and toxicity (ADMET) pharmacokinetic properties, and had been subjected to drug toxicity prediction.It formed hydrogen bonds with Ser15 and alkyl bonds with Met87 and Lys411, with a binding energy of -4.7 kcal/mol.This monoterpene (73) could form a hydrogen bond with Gly110 and an alkyl bond with Lys152 of SARS-CoV-2 3CL pro , with a binding energy of -6.4 kcal/mol.Nevertheless, when targeting the ACE2 protein, only alkyl bonding was observed with Ile106 and Lys103, and the binding energy was -5.6 kcal/mol.Umashankar et al. [67] deciphered the potential natural bioactive anti-SARS-CoV-2 compounds from eight traditional Indian medicinal plants and a vast number of phytochemical moieties.The authors included compounds from Z. officinale and C. longa in the docking and simulation analysis.Among the compounds from different libraries, geraniin (74) (-8.2 kcal/mol) from Z. officinale and O-demethyldemethoxycurcumin (75) (-8 kcal/mol) from C. longa displayed a suitable binding energy through the formation of hydrogen bonds and hydrophobic interactions with the favourable residues on receptor binding domain (RBD) of spike glycoprotein, particularly the glycosylation sites.Viral glycosylation plays a role in viral evasion and replication, thus contributing to the pathogenesis of SARS-CoV-2 in the human body [75,76].Because the complex formed between the viral spike protein and O-demethyldemethoxycurcumin (75) was more stable (ligand root mean square deviation (RMSD) of 1.0-2.5 Å) and exhibited prominent ligand interactions, thus the authors considered it the best-hit compound.The intermolecular interactions between the compound and the hotspots of the ACE2 binding site and the residues of the glycosylation site on the RBD as well as the optimal conformation during the simulation process, indicated its function as a dual-acting inhibitory drug against ACE2 interactions and glycosylation of spike protein.Babaeekhou et al. [62] identified dereplicated bioactive compounds from Z. officinale via molecular networking and employed molecular docking to estimate their binding affinity to three SARS-CoV-2 targets (Fig. 12).The included targets were RBD-ACE2 complex (PDB: 6VW1) [63], spike glycoprotein with the RBD (PDB: 6VSB) [64] and M pro protein structures (PDB: 6LU7 and PDB: 6M03) [65].From the virtual analysis, a flavonoid named 3-[(2S,3R,4S,5S,6R)-4, 5-dihydroxy-6-(hydroxymethyl)-3-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl] oxyoxan-2-yl]oxy-2-(3,4-dihydroxyphenyl)-5-hydroxy-7-methoxychromen-4-one (76) (-9.27 kcal/mol) and sissostrin (77) (-8.643 kcal/mol) had the highest affinity scores for 6VW1, while curcumin (25) (-10.126kcal/mol) presented the best docking score for 6M03.The flavonoid ( 76) also exhibited significant binding affinity to 6VSB (-9.96 kcal/mol), and the docking analysis for 6LU7 indicated the lowest binding energy (-9.399 kcal/mol) for sissostrin (77).The authors postulated that hydrogen bonds, pipi interactions, and ionic bonds between phytoligands and the viral binding sites could be the mechanisms for inhibiting viral entry and replication.Hence, novel natural drugs might represent a way to manage SARS-CoV-2 infections.
Other than the SARS-CoV-2 virus, Narusaka et al. worked with proanthocyanidins (PACs) (81), the major polyphenolic polymers with flavan-3-ols extracted from Alpinia zerumbet (Pers.)B.L.Burtt & R.M.Sm., by examining its antiviral effects on the influenza A virus and porcine epidemic diarrhoea virus (PEDV) through the cytopathic effect (CPE) assay [81].Within the in vitro CPE study, the potent antiviral activity of PACs (81) against influenza A virus has been uncovered, denoted by decreasing the viral titre by >3 logs at 0.1 mg/mL via calculation of 50% endpoint dilution (TCID 50 /mL).Moreover, the PACs (81) at 0.1 mg/mL also successfully decreased the viral titre of PEDV, a surrogate for human coronavirus, especially SARS-CoV-2, by >4 logs as compared to the control.PACs (81) could effectively inactivate both tested viruses in a dose-dependent manner.In another research work conducted by Konappa et al., the group adopted a molecular docking technique to screen the binding affinity of serverogenin acetate (58) on viral target protein 1REV, which is the HIV-1 reverse transcriptase [72].Interaction between the compound and viral protein through hydrogen-bond formation by Gln91 with the best binding pose and binding energy (-90.53kcal/mol) has recommended the isolation and purification via bioassay-guided fractionation of this compound from Amomum nilgiricum V.P.Thomas & M.Sabu for its antiviral potential (Figs. 13-16).

DISCUSSION
Currently, commercially available antibacterial agents are overused throughout the world to inhibit the growth of pathogenic bacteria.This has resulted in the evolution of resistance mechanisms to various prescription antibiotics, presumably through chromosomal mutations or the transmission of exogenous resistance genes [82,83].Over time, an increasing number of multidrug-resistant bacteria inhibit or suppress the antibacterial activity of antibiotics and devastatingly affect their efficacy [84,85].Six nosocomial bacterial species are specified in the ESKAPE acronym: the gram-positive bacteria Enterococcus faecium and S. aureus, and the gram-negative bacteria K. pneumoniae, Acinetobacter baumannii, Enterobacter spp.and P. aeruginosa.These species have been commonly described as being highly virulent and exhibiting antibiotic resistance patterns.Considering the studies included in this scoping review, S. aureus has been the most researched gram-positive bacteria.Several compounds derived from Zingiberaceae species, including A. conchigera, Z. montanum and Z. officinale, exerted an antibacterial effect on the opportunistic pathogen MRSA [48,50,68].
Similarly, a growing number of antifungal drug-resistant strains have resulted in fatal fungal infections, attributable to the widespread use of antifungals for treatment and preventive purposes.This condition is explained by the activation of protective stress response pathways following exposure to antifungals, as opposed to the plasmid-mediated transmission of resistance genes typically observed in the bacterial community [86].Aspergillus, Cryptococcus, Candida and Pneumocystis are the major genera of human pathogenic fun-gi.Targeted therapy implemented for mucosal or invasive fungal infections caused by these fungi undoubtedly contributes to the development of resistant strains [87].The data compiled in this review has shown that most of the compounds derived from Z. officinale have antifungal effects on Aspergillus and Candida species [45,57].
Viruses may deliberately acquire resistance to existing antiviral treatments by undergoing genomic mutations during the replication process [88].Viruses typically replicate in animals; therefore, exposing animal reservoirs to an environment containing potential antiviral drugs may hasten the establishment of antiviral drug resistance.Some viruses associated with human diseases have been reported to show resistance towards antiviral medications, including human immunodeficiency virus [88], hepatitis B virus [89], influenza virus [90], hepatitis C virus [91] and herpes simplex virus [92,93].Intriguingly, oligomers or polymers of monomeric flavan-3-ols named proanthocyanidins (81) extracted from A. zerumbet could reduce the titre of influenza A virus, indicating the antiviral properties of polyphenolic compounds from plants [81].Based on the studies included in this review, the scientific community emphasises medicinal herbs or natural plant-derived products with functional phytochemicals as an innovative therapeutic approach to address microbial infections, especially those with resistance issues.Various natural bioactive compounds isolated from plant extracts have been extrapolated and applied in several fields involving the envi-ronmental, medical and food industries.Antimicrobial bioactive compounds from herbal medicines can exert growth inhibition or eradication effects on bacteria, fungi, viruses and protozoa via distinct mechanisms, as opposed to the currently used antimicrobials; to a certain extent, they may possess relevant therapeutic value in treating diseases caused by resistant microbial strains [94].The diverse or chemically com-plex bioactive constituents of plants are relatively more therapeutically effective than manufactured drugs, have fewer adverse effects, and limit the likelihood of developing resistance [95].
The scientific justification for the use of herbal materials and the discovery of novel lead compounds for conventional single chemical entities (SCEs) are the two main foci of ethnopharmacological research in the pharmaceutical sector [96].Obtaining active fractions from plant extracts through bioassay-guided approaches and the subsequent isolation of pure bioactive compounds are fundamental scholarly and commercial research practices.Therefore, biologically active constituents and/or their derivatives as well as synthetic products based on the chemical structure of these phytochemicals, could all be components of SCEs.Nevertheless, to be approved as an alternative antimicrobial agent, substantial clinical trials must be carried out with a sufficient number of patients with drug-resistant diseases or novel microbial infections.Consideration must be given to thorough in vivo research on bioactive compounds with positive antimicrobial activity and minimal toxicity before the validation phase.The use of in vivo models to evaluate the antimicrobial activity of pure phytochemicals and structurally modified compounds has yet to be widely adopted [94].
COVID-19 pandemic still represents a human health threat.SARS-CoV-2 is the etiological agent of COVID-19 and has rapidly disseminated around the globe.Currently, no effective and specific therapeutic agent is available for this infectious disease, even though innumerable laboratory and clinical trials have been implemented to seek effective antiviral agents against it [97].This may be because of the selective effects on specific groups of patients or, in the worst-case scenario, there are little or no therapeutic benefits in patients with COVID-19 in terms of overall mortality, the hospitalisation duration and the requirement for ventilation [98].Nonetheless, research on the repurposing of existing plant-based compounds, either naturally or synthetically acquired, has been carried out in response to COVID-19 and other emerging viral infections rather than executing de novo synthesis of novel antiviral agents.Furthermore, these phytoextracts or derived phytocompounds have been highlighted as emergency medicinal agents during epidemics or pandemics to control infections caused by novel viruses [99].
Based on our literature search, in vitro experiments have been implemented most often to investigate the antimicrobial efficacy of compounds from the Zingiberaceae family against bacterial and fungal species, whereas in silico methods have been used to study the antiviral potential of the compounds through binding affinity to the target sites, particularly SARS-CoV-2.No information is available regarding the antimicrobial activity of active compounds using in vivo models and clinical trials.in vitro studies are cell-based experiments that are usually employed in the preliminary stages of screening; however, the biocompatibility of compounds cannot be determined through this type of study.Ac-cording to the retrieved data, there are substantial variations in the experimental settings for the isolation, stepwise synthesis and antimicrobial testing of compounds from Zingiberaceae plants, thus presenting diverse investigational alternatives for in vivo experiments using animal models.Despite their complexity and expense, in vivo studies are crucial to elucidate the antimicrobial efficacy and toxicity of potential compounds.Based on our findings, in vivo studies and clinical trials that test these Zingiberaceae phytochemicals against microbial infections are needed.
In silico studies are usually performed through computer simulations to examine the interaction between natural therapeutic ligands and target receptors, thereby reducing the cost of conducting mass laboratory work and simultaneously accelerating the drug discovery process.This approach relies on high-throughput molecular docking to select the potential hits after narrowing down the search for prospective lead entities from a vast number of compound databases [100].Lipinski's rule of five refers to the physicochemical properties of an ideal drug and predicts its drug likeness based on the criteria they should meet: hydrogen bond donors ≤5, hydrogen bond acceptors ≤10, molecular mass <500 Da and partition coefficient (log P) ≤5.As evidenced by the considerable number of studies in this review pertaining to SARS--CoV-2 in silico investigations, this technique has been widely attempted to search for potential COVID-19 treatments to alleviate this pandemic.Although the scientific community has been prompted to create in vitro and in vivo experimental conditions for COVID-19 research, an initial step using in silico methods to examine the therapeutic efficacy of diverse plant-based compounds against possible targets of SARS-CoV-2 structures is crucial.The essential targets of SARS-CoV-2 mentioned in the included studies are 3C-like protease (main protease) and papain-like protease, which play a pivotal role in initiating coronavirus replication by forming a functional replicase complex, whereas the spike protein primarily functions in receptor recognition and eases the process of cell membrane fusion [101,102].Besides, as SARS-CoV-2 is an RNA virus, a virus-specific enzyme known as RNA-dependent RNA polymerase -which regulates viral genome replication and transcription -could also be a potential therapeutic target [59].Consequently, the phytoligands with the greatest potential antiviral efficacy, as indicated by negative binding energy to the aforementioned viral targets, could be subjected to in vitro and in vivo research for further validation.
Based on our search results, compounds from Z. officinale have garnered the most interest for their antiviral potential against SARS-CoV-2, either directly towards the viral structures or indirectly by inhibiting viral cellular targets.Another in silico study collectively revealed the antibacterial, antifungal and antiviral properties of serverogenin acetate (58) from A. nilgiricumvia molecular docking [72].Serverogenin acetate (58) is the only bioactive component included in this review that has been evaluated for antibacterial, antifungal and antiviral activities.It demonstrated favourable ligand-protein interactions with the bacterial 5iwm, fungal 4i9p and viral 1rev target proteins.
Hydrophobic compounds have difficulty crossing the hydrophilic cell wall of gram-negative bacteria, which creates a formidable permeability barrier.On the other hand, hydrophilic compounds are unable to penetrate the inner membrane of gram-negative bacteria, which contains a glycerophospholipid bilayer [103].As a result, the compounds should have a lower antibacterial efficacy against gram-negative than gram-positive bacteria.However, 6-shogaol (31), a hydrophobic ginger polyphenol from Z. officinale, had superior antibacterial activity against gram-negative bacteria compared with 6-gingerol (32), regardless of the structural barrier of the tested bacteria [48].This could be due to the presence of a hydroxyl group in 6-gingerol (32), which reduces the compound's lipophilicity and cell membrane permeability, resulting in decreased cell bioavailability [104].In addition, 6-shogaol (31) could inhibit C. auris planktonic cells and biofilm in a concentration-dependent manner [57].Etlingerin (24) isolated from E. pubescens showed antibacterial activity against S. aureus and B. subtilis by altering bacterial membrane permeability and, consequently, mediating intracellular leakage in a dose-dependent manner and causing cell death, suggesting the antibacterial mechanism of this compound.
The ability of phytochemicals or their synthetic analogues to exert antimicrobial effects is influenced by their shape, size, structure and chemical properties to reach the targeted site of action.Compounds synthesised from naturally occurring bioactive constituents have modified chemical structures that improve or impair their antimicrobial efficacy.The synthetic variants of zingerone (40)(41)(42)(43)(44) demonstrated the most potent antibacterial effect against the tested gram-negative bacteria, attributable to the modification of carbonyl functionality in the side chain of its precursor [46].Other than that, five synthetic derivatives of the bioflavonoid pinostrobin (5)(6)(7)(8)(9) exhibited enhanced antibacterial activity against a panel of bacterial species, including S. aureus, B. subtilis, P. aeruginosa and E. coli, owing to the substitution of the flavone ring system of pinostrobin ( 4) with prenyl groups.This substitution increased the lipophilicity of the analogues, thus facilitating the interaction between compounds and bacterial membranes [47].Generally, it is necessary to determine how to strategically modify the structure of the compounds, which in turn could improve their affinity and selectivity for the targets, allowing biological activities to take place at the molecular level.
In one study, the authors claimed that zerumbone (15) isolated from Z. zerumbet showed more effective antibacterial and antifungal activity against the tested bacteria and fungi compared with fresh and dry rhizome essential oils, whereas another study stated that purified curcumin obtained from C. caesia exhibited greater antibacterial effect against gram-positive and gram-negative bacteria than the crude extract [52,53].Greater antifungal and antibacterial activity of the plant crude extracts, essential oils or fractions may be due to the combined mechanisms of action of numerous classes of bioactive constituents.Nevertheless, their antimicrobial activities were lower than those of the individual isolated compounds in certain studies, suggesting it is necessary to isolate compounds to minimise the underlying antagonistic interactions among the bioactive compounds [105].Apart from utilising a single product, bioactive constituents from herbal plants or their related synthetic derivatives could be applied in combination with each other or even with commercially available antimicrobial agents to restore their antimicrobial effects and to circumvent the resistance problem [84].Lariciresinol (45), a lignin belonging to phenylpropanoid isolated from Z. officinale, produced a synergistic antibacterial effect against S. enterica ser.Typhimurium strains when co-administered with a tetracycline antibiotic and lowered the MIC of that antibiotic [56].
There are a few limitations to this scoping review.We included 'Zingiber' and 'Zingiber officinale Roscoe' in the search query because this genus includes true gingers within Zingiberaceae and Z. officinale is the most well-known garden ginger and a representative of this family [106].As a result, we included more studies that evaluated Z. officinale in this review.Because Zingiberaceae covers a vast array of species and compounds, we included the classes of representative bioactive compounds available in its genera in the keyword search rather than incorporating each individual species, bioactive compound and synthetic analogue into the search.Even though we made every attempt to conduct a thorough search, we may have overlooked certain studies that focused on the bioactive constituents of Zingiberaceae plants or their synthetic derivatives.Moreover, a systematic review and meta-analysis should be conducted to collect the highest level of evidence regarding the antimicrobial potential of compounds isolated from Zingiberaceae members [107].Despite these limitations, based on the current evidence, natural compounds from the discussed Zingiberaceae species and their synthetic analogues could be alternative agents for the treatment of microbial infections.

CONCLUSION
Accumulating evidence on the antimicrobial activity of bioactive compounds from Zingiberaceae plants and their synthetic derivatives has highlighted their potential as prospective antimicrobial agents.Nevertheless, the compounds from each included Zingiberaceae species should be tested on diverse groups of microorganisms, including resistant strains, to examine their potential antimicrobial efficacy.In fact, combining plant-derived compounds or their structurally modified analogues with commercially available antimicrobial agents could be a promising strategy to overcome the challenges elicited by resistant microbes.Moreover, more research should be carried out to elucidate the antimicrobial mechanisms of action, pharmacodynamics and pharmacokinetics of these compounds.Substantial in vivo studies and clinical trials are warranted to translate their roles into therapeutic practice in humans.The development of novel antimicrobial agents should consider the factors that may influence the efficacy of either bioactive constituents or synthetic analogues, such as tissue penetration, bioavailability and drug plasma levels.

STANDARDS OF REPORTING
PRISMA guidelines and methodology were followed.

Fig. ( 10 ).
Fig. (10).Microorganisms that were evaluated in the included studies.(A higher resolution / colour version of this figure is available in the electronic copy of the article).
Fig. (11).Methods used for the assessment of antimicrobial activities.(A higher resolution / colour version of this figure is available in the electronic copy of the article).

Fig
Fig. (12).Three compounds from Zingiber officinale Roscoe were docked to the SARS-CoV-2 targets with prominent interactions, which included (A) the RBD-ACE2 complex (PDB: 6VW1), (B) pre-fusion 2019-nCoV spike glycoprotein with a single receptor-binding domain (PDB: 6VSB) and two M pro structures, namely (C) PDB: 6LU7 and (D) PDB: 6M03 [62].(A higher resolution / colour version of this figure is available in the electronic copy of the article).